Table 1. Examples of cancer gene mutation orders with a predicted probability greater than random chance.
| Order | Probability | Order | Probability |
| APC→BRCA2 | 0.99932 | APC→ATM→KRAS | 0.39011 |
| APC→FBXW7 | 0.99675 | APC→KRAS→ATM | 0.41748 |
| APC→KRAS | 0.95281 | APC→BRAF→TP53 | 0.20884 |
| APC→NOTCH2 | 0.99906 | APC→TP53→BRAF | 0.34198 |
| APC→PTEN | 0.99986 | TP53→APC→BRAF | 0.2958 |
| APC→SMARCA4 | 0.99934 | APC→KRAS→TP53 | 0.33317 |
| APC→TP53 | 0.65624 | APC→TP53→KRAS | 0.32532 |
| ARID1A→ATM | 0.99991 | TP53→APC→KRAS | 0.18769 |
| ARID1A→CTNNB1 | 0.99987 | APC→MLL3→PTEN | 0.49936 |
| ARID1A→PTEN | 0.99966 | APC→PTEN→MLL3 | 0.49797 |
| ARID2→CTNNB1 | 0.99992 | CREBBP→KRAS→ARID1A | 0.36621 |
| BRAF→FBXW7 | 0.99994 | CREBBP→ARID1A→KRAS | 0.56109 |
| BRAF→PTEN | 0.99792 | CREBBP→CTNNB1→SMARCA4 | 0.27984 |
| CREBBP→BRCA2 | 0.9995 | CREBBP→SMARCA4→CTNNB1 | 0.71849 |
| CREBBP→CTNNB1 | 0.99906 | MLL3→SMARCA4→EP300 | 0.49603 |
| CTNNB1→SMARCA4 | 0.7542 | MLL3→EP300→SMARCA4 | 0.4967 |
| EZH2→CARD11 | 0.99922 | PIK3CA→SMARCA4→CTNNB1 | 0.46455 |
| EZH2→CTNNB1 | 0.96595 | PIK3CA→CTNNB1→SMARCA4 | 0.52713 |
| KRAS→FBXW7 | 0.75719 | TP53→MLL3→ARID1A | 0.48265 |
| KRAS→PTEN | 0.99874 | TP53→ARID1A→MLL3 | 0.45573 |
| MLL2→CTNNB1 | 0.99989 | TP53→MLL3→ARID2 | 0.4851 |
| MYH11→SMARCA4 | 0.99606 | TP53→ARID2→MLL3 | 0.46217 |
| NOTCH2→ARID1A | 0.99964 | TP53→CTNNB1→ATM | 0.49888 |
| NRAS→SMARCA4 | 0.95881 | TP53→ATM→CTNNB1 | 0.50012 |
| PIK3CA→ARID1A | 0.99971 | TP53→ROS1→BRAF | 0.73047 |
| PIK3CA→EP300 | 0.99954 | TP53→BRAF→ROS1 | 0.26871 |
| TP53→ARID1A | 0.99985 | TP53→PIK3CA→BRCA2 | 0.49745 |
| TP53→AKAP9 | 0.99941 | TP53→BRCA2→PIK3CA | 0.49757 |
| TP53→ARID2 | 0.99985 | TP53→EZH2→CREBBP | 0.47725 |
| TP53→ATM | 0.99974 | TP53→CREBBP→EZH2 | 0.52201 |
| TP53→BRAF | 0.99937 | TP53→MLL2→CREBBP | 0.56795 |
| TP53→BRCA2 | 0.99827 | TP53→CREBBP→MLL2 | 0.43152 |
| TP53→CARD11 | 0.99926 | TP53→NOTCH2→CREBBP | 0.50977 |
| TP53→CREBBP | 0.99989 | TP53→CREBBP→NOTCH2 | 0.4884 |
| TP53→CTNNB1 | 0.99984 | TP53→FBXW7→CTNNB1 | 0.47758 |
| TP53→EP300 | 0.99894 | TP53→CTNNB1→FBXW7 | 0.47344 |
| TP53→EZH2 | 0.99985 | TP53→KRAS→CTNNB1 | 0.42094 |
| TP53→KRAS | 0.83612 | TP53→CTNNB1→KRAS | 0.4181 |
| TP53→MLL | 0.99992 | TP53→MLL2→EZH2 | 0.5875 |
| TP53→MLL2 | 0.9999 | TP53→EZH2→MLL2 | 0.41196 |
| TP53→MLL3 | 0.98377 | TP53→KRAS→FBXW7 | 0.38181 |
| TP53→MYH11 | 0.99954 | TP53→FBXW7→KRAS | 0.31798 |
| TP53→NRAS | 0.94242 | TP53→PIK3CA→KRAS | 0.40396 |
| TP53→PIK3CA | 0.99789 | TP53→KRAS→PIK3CA | 0.36917 |
| TP53→PTEN | 0.99989 | TP53→PIK3CA→MYH11 | 0.49797 |
| TP53→SMARCA4 | 0.99988 | TP53→MYH11→PIK3CA | 0.49427 |
The examples in the table are selected based on that the genes have a mutant frequency greater than 40 in the COSMIC database to show the estimation for the common cases. Due to the limited space, the prediction for the samples with more than 3 mutant cancer genes is not shown. Refer to Table S3 for a complete result.
The random chance is 1/n!, where n is the number of mutant cancer genes in the sample.
Note, any two samples with the same set of mutant genes have identical predicted results.